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Contents

Background

Bacteria are typically found attached to and living in close association with surfaces. During the bacterial lifespan, a bacterium is subjected to frequent shear-forces. In the crudest sense, bacterial adhesins serve as anchors allowing bacteria to overcome these environmental shear forces, thus remaining in their desired environment. However, bacterial adhesins do not serve as a sort of universal bacterial Velcro. Rather, they act as specific surface recognition molecules, allowing the targeting of a particular bacterium to a particular surface such as root tissue in plants, lacrimal duct tissues in mammals, or even tooth enamel.[2]

Most fimbria of gram-negative bacteria function as adhesins, but in many cases it is a minor subunit protein at the tip of the fimbriae that is the actual adhesin. In gram-positive bacteria, a protein or polysaccharide surface layer serves as the specific adhesin. To effectively achieve adherence to host surfaces, many bacteria produce multiple adherence factors called adhesins.

Structures

Through the mechanisms of evolution, different species of bacteria have developed different solutions to the problem of attaching receptor specific proteins to the bacteria surface. Today many different types and subclasses of bacterial adhesins may be observed in the literature.

The typical structure of a bacterial adhesion is that of a fimbria or pili.[2] The bacterial adhesion consists primarily of an intramembranous structural protein which provides a scaffold upon which several extracellular adhesins may be attached.[2] However, as in the case of the CFA1 fimbriae, the structural protein itself can sometimes act as an adhesion if a portion of the protein extends into the ECM.

FimH Adhesin â€” Structure

The best characterized bacterial adhesin is the type 1 fimbrial FimH adhesin. This adhesin is responsible for D-mannose sensitive adhesion.[2] The bacterium synthesizes a precursor protein consisting of 300 amino acids then processes the protein by removing several signal peptides ultimately leaving a 279 amino acid protein.[2] Mature FimH is displayed on the bacterial surface as a component of the type 1 fimbrial organelle.[2]

In 1999, the structure of FimH was resolved via x-ray crystallography. FimH is folded into two domains. The N terminal adhesive domain plays the main role in surface recognition while the C-terminal domain is responsible for organelle integration.[3] A tetra-peptide loop links the two domains. Additionally, a carbohydrate-binding pocket has been identified at the tip of the N-terminal adhesive domain.[3] This basic structure is conserved across type 1 fimbrial adhesins though recent studies have shown that in vitro induced mutations can lead to the addition of C-terminal domain specificity resulting in a bacterial adhesion with dual bending sites and related binding phenotypes.[4]

Adhesins as Virulence Factors

The majority of bacterial pathogens exploit specific adhesion to host cells as their main virulence factor. â€œA large number of bacterial adhesins with individual receptor specificities have been identified.â€[2] Many bacterial pathogens are able to express an array of different adhesins. Expression of these adhesins at different phases during infection play the most important role in adhesion based virulence.[2] Numerous studies have shown that inhibiting a single adhesin in this coordinated effort can often be enough to make a pathogenic bacterium non-virulent. This has led to the exploration of adhesin activity interruption as a method of bacterial infection treatment.

Vaccines based on Adhesins

The study of adhesins as a point of exploitation for vaccines comes from early studies which indicated that an important component of protective immunity against certain bacteria came from an ability to prevent adhesin binding.[5] Additionally, Adhesins are attractive vaccine candidates because they are often essential to infection and are surface-located, making them readily accessible to antibodies.

The effectiveness of anti-adhesin antibodies is illustrated by studies with FimH, the adhesin of uropathogenic Escherichia coli (UPEC).Work with E. coli stems from observations of human acquired immunity. Children in third world countries may suffer from several episodes of E. coli associated diarrhea during the first three years of life. If the child survives this initial period of susceptibility, infection rates typically drop substantially. Field studies show that this acquired immunity is directed primarily against bacterial adhesins.[2]

Recent studies from Worchester Polytechnic institute show that the consumption of cranberry juice cocktail may inhibit the action of UPEC adhesins. Using atomic force microscopy researchers have shown that adhesion forces decrease with time following cranberry juice cocktail consumption.[6] This type of research has opened the door to further exploration of orally administered vaccines which exploit bacterial adhesins.

A number of problems create challenges for the researcher exploring the anti-adhesin immunity concept. First and foremost among these problems is the large number of different bacterial adhesins which target the same human tissues. Further problems arise when considering an individual bacteriumâ€™s ability to produce multiple different types of adhesins most of which are produced at different times, in different places, and in response to different environmental triggers.[2] Finally, the most pressing problem becomes evident when considering that many adhesins present as different immunologically distinct antigentic varieties, even within the same clone (as is the case in Neisseria gonorrhoeae).[7]

Despite these challenges, progress is being made in the creation of anti-adhesion vaccines. In animal models, passive immunization with anti FimH-antibodies and vaccination with the protein significantly reduced colonization by UPEC.[8] Moreover, the Bordetella pertussis adhesins FHA and pertactin are components of 3 of the 4 acellular pertussis vaccines currently licensed for use in the U.S. Additionally, anti-adhesion vaccines are being explored as a solution to urinary-tract infections (UTIs). The use of synthetic FimH adhesion peptides was shown to prevent urogenital mucosal infection by E. coli in mice.[9]

N. gonorroheae

N. gonorrhoeae is host restricted almost entirely to humans.[2] â€œExtensive studies have established type 4 fimbrial adhesins of N. gonorrhoeae virulence factors.â€[2] These studies have shown that only strains capable of expressing fimbriae are pathogenic. High survival of polymorphonuclear neutrophils (PMNs) characterizes Neisseria gonorrhoeae infections. Additionally, recent studies out of Stockholm have shown that Neisseria can hitchhike on PMNs using their adhesin pili thus hiding them from neutrophil phagocytic activity. This action facilitates the spread of the pathogen throughout the epithelial cell layer.[13]

E. coli

Escherichia coli strains most known for causing diarrhea can be found in the intestinal tissue of pigs and humans where they express the K88 and CFA1.[14] to attach to the intestinal lining. Additionally, UPEC causes about 90% of urinary tract infections.[15] Of those E. coli which cause UTIs, 95% express type 1 fimbriae. FimH in E. coli overcomes the antibody based immune response by natural conversion from the high to the low affinity state. Through this conversion, FimH adhesion may shed the antibodies bound to it. Escherichia coli FimH provides an example of conformation specific immune response which enhances impact on the protein.[15] By studying this particular adhesion, researchers hope to develop adhesion-specific vaccines which may serve as a model for antibody-mediation of pathogen adhesion.[15]

"DUF" families are annotated with the
Domain of unknown function Wikipedia article. This is a general
article, with no specific information about individual Pfam DUFs. If
you have information about this particular DUF, please let us know
using the "Add annotation" button below.

This bacterial family of proteins shows structural similarity to other pectin lyase families. Although structures from this family align with acetyl-transferases, there is no conservation of catalytic residues found. It is likely that the function is one of cell-adhesion. In PDB:3jx8 it is interesting to note that the sequence of contains several well defined sequence repeats, centred around GSG motifs defining the tight beta turn between the two sheets of the super-helix; there are 8 such repeats in the C-terminal half of the protein, which could be grouped into 4 repeats of two. It seems likely that this family belongs to the superfamily of trimeric auto-transporter adhesins (TAAs), which are important virulence factors in Gram-negative pathogens [1] [2]. In the case of Parabacteroides distasonis, which is a component of the normal distal human gut microbiota, TAA-like complexes probably modulate adherence to the host (information derived from TOPSAN).

External database links

Domain organisation

Below is a listing of the unique domain organisations or architectures in which
this domain is found.
More...

The graphic that is shown by default represents the longest sequence
with a given architecture. Each row contains the following information:

the number of sequences which exhibit this architecture

a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one Gla
domain, followed by two consecutive EGF domains, and
finally a single Trypsin domain

a link to the page in the Pfam site showing information about the
sequence that the graphic describes

Note that you can see the family page for a particular domain by
clicking on the graphic. You can also choose to see all sequences which
have a given architecture by clicking on the Show link
in each row.

Finally, because some families can be found in a very large number of
architectures, we load only the first fifty architectures by default.
If you want to see more architectures, click the button at the bottom
of the page to load the next set.

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Pfam Clan

This family is a member of clan Adhesin
(CL0204),
which has the following description:

This superfamily includes a variety of bacterial adhesins that have a jelly-roll beta-barrel fold [1]. These domains are involved in sugar recognition.

Alignments

We store a range of different sequence alignments for families. As well
as the seed alignment from which the family is built, we provide the
full alignment, generated by searching the sequence database using the
family HMM. We also generate alignments using four
representative proteomes (RP) sets, the NCBI sequence database,
and our metagenomics sequence database.
More...

There are various ways to view or download the sequence alignments that
we store. We provide several sequence viewers and a plain-text
Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed

the curated alignment from which the HMM for the family is
built

full

the alignment generated by searching the sequence database
using the HMM

Viewing

a Java applet developed at the University of Dundee. You will
need Java installed
before running jalview

HTML

an HTML page showing the whole alignment.Please
note: full Pfam alignments can be very large. These
HTML views are extremely large and often cause problems for browsers.
Please use either jalview or the Pfam viewer if you have trouble
viewing the HTML version

PP/Heatmap

an HTML-based representation of the alignment, coloured according to
the posterior-probability (PP) values from the HMM. As for the standard HTML
view, heatmap alignments can also be very large and slow to render.

Pfam viewer

an HTML-based viewer that uses
DAS
to retrieve alignment fragments on request

Reformatting

You can download (or view in your browser) a text representation of a
Pfam alignment in various formats:

Selex

Stockholm

FASTA

MSF

You can also change the order in which sequences are listed in the
alignment, change how insertions are represented, alter the characters
that are used to represent gaps in sequences and, finally, choose
whether to download the alignment or to view it in your browser
directly.

Downloading

You may find that large alignments cause problems for the viewers and
the reformatting tool, so we also provide all alignments in Stockholm
format. You can download either the plain text alignment, or a gzipped
version of it.

View options

We make a range of alignments for each Pfam-A family. You can see a
description of each
above.
You can view these alignments in various ways but please note that some
types of alignment are never generated while others may not be available
for all families, most commonly because the alignments are too large to
handle.

Seed(115)

Full(1939)

Representative proteomes

NCBI(2140)

Meta(136)

RP15(83)

RP35(243)

RP55(426)

RP75(499)

Jalview

View

View

View

View

View

View

View

View

HTML

View

View

View

View

View

View

PP/heatmap

1

View

View

View

View

View

Pfam viewer

View

View

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available,
not generated,
— not available.

Format an alignment

Seed(115)

Full(1939)

Representative proteomes

NCBI(2140)

Meta(136)

RP15(83)

RP35(243)

RP55(426)

RP75(499)

Alignment:

Format:

Order:

TreeAlphabetical

Sequence:

Inserts lower caseAll upper case

Gaps:

Download/view:

DownloadView

Download options

We make all of our alignments available in Stockholm format.
You can download them here as raw, plain text files or as
gzip-compressed files.

You can also
download a FASTA format file containing the
full-length sequences for all sequences in the full alignment.

External links

MyHits provides a
collection of tools to handle multiple sequence alignments. For example,
one can refine a seed alignment (sequence addition or removal,
re-alignment or manual edition) and then search databases for remote
homologs using HMMER3.

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HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a
quick overview of the properties of an HMM in a graphical form. You can
see a more detailed description of HMM logos and find out how you can
interpret them
here.
More...

If you find these logos useful in your own work, please consider citing
the following article:

Trees

This page displays the phylogenetic tree for this family's seed
alignment. We use
FastTree
to calculate neighbour join trees with a local bootstrap based on 100
resamples (shown next to the tree nodes). FastTree calculates
approximately-maximum-likelihood phylogenetic trees from our seed
alignment.

Curation and family details

This section shows the detailed information about the Pfam family. You
can see the definitions of many of the terms in this section in the
glossary and a fuller
explanation of the scoring system that we use in the
scores section of the
help pages.

Currently selected:

This visualisation provides a simple graphical representation of
the distribution of this family across species. You can find the
original interactive tree in the
adjacent tab.
More...

This chart is a modified "sunburst" visualisation of
the species tree for this family. It shows each node in the
tree as a separate arc, arranged radially with the superkingdoms
at the centre and the species arrayed around the outermost
ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each
sequence that has a match to this family. For each node in the
resulting tree, we draw an arc in the sunburst. The radius of
the arc, its distance from the root node at the centre of the
sunburst, shows the taxonomic level ("superkingdom",
"kingdom", etc). The length of the arc represents
either the number of sequences represented at a given level, or
the number of species that are found beneath the node in the
tree. The weighting scheme can be changed using the sunburst
controls.

In order to reduce the complexity of the representation, we
reduce the number of taxonomic levels that we show. We consider
only the following eight major taxonomic levels:

superkingdom

kingdom

phylum

class

order

family

genus

species

Colouring and labels

Segments of the tree are coloured approximately according to
their superkingdom. For example, archeal branches are coloured
with shades of orange, eukaryotes in shades of purple, etc. The
colour assignments are shown under the sunburst controls. Where
space allows, the name of the taxonomic level will be written on
the arc itself.

As you move your mouse across the sunburst, the current node
will be highlighted. In the top section of the controls panel we
show a summary of the lineage of the currently highlighed node.
If you pause over an arc, a tooltip will be shown, giving the
name of the taxonomic level in the title and a summary of the
number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily
handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of
the main eight levels that we display. For example, Bos
taurus is not assigned an order in the NCBI taxonomic tree.
In such cases we mark the omitted level with, for example,
"No order", in both the tooltip and the lineage
summary.

Unmapped species names

The tree is built by looking at each sequence in the full
alignment for the family. We take the name of the species given
by UniProt and try to map that to the full taxonomic tree from
NCBI. In some cases, the name chosen by UniProt does not map to
any node in the NCBI tree, perhaps because the chosen name is
listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst
tree, we group them together in a separate branch (or segment of
the sunburst tree). Since we cannot determine the lineage for
these unmapped species, we show all levels between the
superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main
taxonomic levels, sequences that are mapped to the sub-species
level in the tree would not normally be shown. Rather than leave
out these species, we map them instead to their parent species.
So, for example, for sequences belonging to one of the
Vibrio cholerae sub-species in the NCBI taxonomy, we
show them instead as belonging to the species Vibrio
cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer
layers of the sunburst. These occur when there are large numbers
of arcs to be drawn in a small space. If an arc is less than
approximately one pixel wide, it will not be drawn and the space
will be left blank. You may still be able to get some
information about the species in that region by moving your mouse
across the area, but since each arc will be very small, it will
be difficult to accurately locate a particular species.

Tree controls

Annotation

Download tree

Selected sequences

(Uncheck all)

View

graphically

as an
alignment

Download

sequence accessions

sequences in FASTA format

The tree shows the occurrence of this domain across different species.
More...

Species trees

We show the species tree in one of two ways. For smaller trees we try
to show an interactive representation, which allows you to select
specific nodes in the tree and view them as an alignment or as a set
of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the
interactive tree when the it becomes larger than a certain limit.
Furthermore, we have found that Internet Explorer can become
unresponsive when viewing some trees, regardless of their size.
We therefore show a text representation of the species tree when the
size is above a certain limit or if you are using Internet Explorer
to view the site.

If you are using IE you can still load the interactive tree by
clicking the "Generate interactive tree" button, but please
be aware of the potential problems that the interactive species tree
can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the
number that are found on all sequences in the alignment.
This total is shown in the purple box.

We also count the number of unique sequences on which each domain is
found, which is shown in green.
Note that a domain may appear multiple times on the
same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the
NCBI
code that is assigned by
UniProt,
allowing us to count the number of distinct sequences on which the
domain is found. This value is shown in the
pink boxes.

We use the NCBI species tree to group organisms according to their
taxonomy and this forms the structure of the displayed tree.
Note that in some cases the trees are too large (have
too many nodes) to allow us to build an interactive tree, but in most
cases you can still view the tree in a plain text, non-interactive
representation. Those species which are represented in the seed
alignment for this domain are
highlighted.

You can use the tree controls to manipulate how the interactive tree
is displayed:

show/hide the summary boxes

highlight species that are represented in the seed alignment

expand/collapse the tree or expand it to a given depth

select a sub-tree or a set of species within the tree and view
them graphically or as an alignment

save a plain text representation of the tree

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Please note: for large trees this can take some time.
While the tree is loading, you can safely switch away from this
tab but if you browse away from the family page entirely, the tree
will not be loaded.

Interactions

There is
1
interaction for this family.
More...

We determine these interactions using
iPfam,
which considers the interactions between residues in three-dimensional
protein structures and maps those interactions back to Pfam families.
You can find more information about the iPfam algorithm in the
journal article that accompanies the website.

Structures

For those sequences which have a structure in the
Protein DataBank, we
use the mapping between UniProt, PDB and Pfam coordinate
systems from the PDBe group, to allow us to map
Pfam domains onto UniProt sequences and three-dimensional protein
structures. The table below
shows the structures on which the DUF2807
domain has been found. There are 35
instances of this domain found in the PDB. Note that there may be
multiple copies of the domain in a single PDB structure, since many
structures contain multiple copies of the same protein seqence.